Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are made from nucleotides and, along with proteins, are present in all known forms of life. They function in encoding, transmitting and expressing genetic information and life forms differ by the order of nucleotides within a DNA or RNA molecule, known as the nucleic acid sequence. Determining the nucleic acids sequences in a sample is known as sequencing.
It is possible to determine the type(s) of life form(s) present in a sample by isolating the genetic material of the life form(s) from the sample, determining the nucleic acid sequence of that genetic material, and using a variety of computational or algorithmic methods to determine the likely sources of that genetic material. Nucleic acid sequences matched to known genomes to determine the type of life form(s) present in the sample.
A microorganism is microscopic organism, such as a bacterium, protozoa, or fungus. A pathogen may be a microbial organism (e.g., a bacterium, phytoplasma, virus, viroid, protozoan, rickettsia, or fungus). Additionally, a pathogen may be a bacterium, phytoplasma, virus, viroid, protozoan, rickettsia, fungus, helminth, parasite, or pest. A microbe is a microorganism, such as a bacterium, that, e.g., causes a disease or fermentation. Interactions between microbes may be exhibit commensalism (one benefits from the other without affecting the other), mutualism (mutually beneficial), amensalism (one is harmed while the other is unaffected), or parasitism (one benefits while the other is harmed) relationships with other organisms. Microbes may change how they affect other organisms, such as a commensal microbe becoming pathogenic under stress. For example, a particular bacteria may be harmonious with a particular fungi, but when the bacteria is stressed and dies off, the fungi may become pathogenic. A microbe that is pathogenic is a microorganism that can produce disease. Typically, a pathogen is an infectious agent such as a virus, bacterium, prion, fungus, viroid, protozoa nematode or parasite families that causes disease in its host. While there are thousands of species of pathogens, only a few dozen pathogens have been sequenced or even studied. It is also possible to have pathogenic host genes.
The nucleic acids of humans is a frequent focus for studies and out of those studies have come tools and processes to make further study of humans much easier. However, assumptions made about similarities of nucleic acid sequences across the human race may not apply to microbes. Similar kinds of assumptions are invalid when sequencing non-human material, making the use of most existing methods and tools inappropriate for non-human study.
When checking a sample for the presence or absence of a particular microbe, existing tools may count the number of nucleic acid sequences in the sample that align 100% to known nucleic acid sequences of that microbe. The nucleic acid sequences in the sample that do not align to that microbe, called unaligned sequences, are not used or even generally retained. Nucleic acid sequences may not align for many reasons, such as the presence of merely one or more mutations that are undetectable by the particular bioinformatics alignment algorithm used.